Daniel A Jacobson

Daniel Jacobson

Distinguished Research Scientist, Computational Systems Biologist

Contact

JACOBSONDA@ORNL.GOV

Bio

We are happy to be the first group to break the Exascale barrier and to have done it for biology.  This project led to us winning the 2018 Gordon Bell Prize (the first ever for Systems Biology). At present, our latest 9.37 Exaflops mixed precision calculation is the fastest scientific calculation ever done anywhere in the world.

https://www.olcf.ornl.gov/2018/06/08/genomics-code-exceeds-exaops-on-su…

https://www.energy.gov/articles/doe-laboratories-win-gordon-bell-prize

My team focuses on the development and subsequent application of mathematical, statistical and computational methods to biological datasets in order to yield new insights into complex biological systems.  Our approaches include the use of Network Theory and Topology Discovery/Clustering, Wavelet Theory, Machine & Deep Learning (amongst others: iterative Random Forests, Deep Neural Networks, etc.) and Linear Algebra (primarily as applied to large-scale multivariate modeling), together with traditional and more advanced computing architectures, such as MPI parallelization.  We make use of various programming languages including C, Python, Perl, and R. Areas of Statistics of particular interest to my lab include the use of both frequentist (parametric and non-parametric) and Bayesian methods as well as the development of new methods for Genome-Wide Association Studies (GWAS) and Phenome-Wide Associations Studies (PheWAS).  These mathematical and statistical methods are applied to various population and (meta)multiomics data sets (Genomics, Phylogenomics, Transcriptomics, Proteomics, Metabolomics, Microbiomics, Viriomics, Phytobiomics, Chemiomics, etc.) individually as well as in combination in an attempt to better understand the functional relationships as well as biosynthesis, signaling, transcriptional, translational, degradation and kinetic regulatory networks at play in biological organisms and communities.

Many of our projects center around studying systems in involved the Center for Bioenergy Innovation (CBI), Plant-Microbial Interfaces (PMI) and Secure Ecosystem Engineering and Design (SEED)  programs at ORNL.  However, we have a broad view of biological complexity and evolution that stretches from viruses to microbes to plants to humans (including cancer and neuroscience) which is reflected by a broad funding portfolio from DOE, NIH, NSF, VA and other sources.

ORNL is home to some of the world’s largest supercomputers. My team uses petascale and exascale computing to analyze and model complex biological systems. Thus, there are excellent opportunities to be involved in the cutting edge of computational systems biology and supercomputing.​

As interdisciplinary and multidisciplinary efforts are more and more critical for scientific discovery, we do maintain a wide network of collaborations from all around the world.

 

Awards

Gordon Bell Prize

Secretary of Energy Honor Award: The Secretary of Energy’s Achievement Award

Joint Citation from the Department of Energy and Department of Veterans Affairs

Oak Ridge National Laboratory, Director’s Award

Oak Ridge National Laboratory, Outstanding Achievement Award

HPCWire Editor’s Choice Award for the Top HPC-enabled Scientific Achievement

Publications

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Other Publications

  1. Muralikrishnan Gopalakrishnan Meena, Matthew J Lane, Joanna Tannous, Alyssa A. Carrell, Paul E Abraham, Richard J Giannone, Mr. Jean-Michel Ane, Nancy P. Keller, Jesse L Labbé, David Kainer, Daniel Jacobson, Tomás A Rush. A guide into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs. PNAS Nexus. Accepted.

 

  1. Jaclyn M. Noshay, Tyler Walker, William G. Alexander, Dawn M. Klingeman, Jonathon Romero, Angelica M. Walker, Erica Prates, Carrie Eckert, Stephan Irle, *David Kainer, and *Daniel A. Jacobson. 2023. Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering. Nucleic Acids Research.

 

  1. Lagergren, J.H., Pavicic, M., Chhetri, H.B., York, L.M., Hyatt, D., Kainer, D., Rutter, E.M., Flores, K., Bailey-Bale, J., Klein, M. and Taylor, G., 2023. Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa. Plant Phenomics. DOI: 10.34133/plantphenomics.0072

 

  1. Bridget S. O’Banion, Piet Jones, Alexander A. Demetros, Brittni R. Kelley, Andrew S. Wagner, Todd B. Reynolds, Jin-Gui Chen, Wellington Muchero, Daniel Jacobson, Sarah L. Lebeis. 2023. Plant myo-inositol transport influences bacterial colonization phenotypes. Current Biology. https://doi.org/10.1016/j.cub.2023.06.057

 

  1. Mirko Pavicic, Angelica M Walker, Kyle A Sullivan, John Lagergren, Ashley Cliff, Jonathon Romero, Jared Streich, Michael R Garvin, John Pestian, Benjamin McMahon, David W Oslin, Jean C Beckham, Nathan A Kimbrel* and Daniel A Jacobson*. 2023. Using Iterative Random Forest to Find Geospatial Environmental and Sociodemographic Predictors of Suicide Attempts. Frontiers in Psychiatry, 14, p.1178633.

 

  1. Scott Atchley, Chris Zimmer, John R. Lange, David E. Bernholdt, Verónica G. Melesse Vergara, Thomas Beck, Michael J. Brim, Reuben Budiardja, Sunita Chandrasekaran, Markus Eisenbach, Thomas Evans, Matthew Ezell, Nicholas Frontiere, Antigoni Georgiadou, Joe Glenski, Philipp Grete, Steven Hamilton, John Holmen, Axel Huebl, Daniel Jacobson, Wayne Joubert, Kim McMahon, Elia Merzari, Stan G Moore, Andrew Myers, Stephen Nichols, Sarp Oral, Thomas Papatheodore, Danny Perez, David M. Rogers, Evan Schneider, Jean-Luc Vay, and P.K. Yeung. 2023. Frontier: Exploring Exascale: The System Architecture of the First Exascale Supercomputer. In The International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’23), November 12–17, 2023, Denver, CO, USA. ACM, New York, NY, USA, 15 pages. https://doi.org/10.1145/3581784.3607089

 

  1. Thaddeus J. Kunkel#, Alice Townsend#, Kyle A. Sullivan, Jean Merlet, Edward H Schuchman, Daniel A. Jacobson*, Andrew P. Lieberman*. 2023. The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells. 14, 3964 (2023). 

 

  1. Patricia Saint-Vincent*, Anna Furches*, Stephanie Galanie, Erica Teixeira Prates, Nan Zhao, Madhavi Martin, Priya Ranjan, Piet Jones, David Kainer, Udaya Kalluri, Jin-Gui Chen, Wellington Muchero, Daniel Jacobson† and Timothy Tschaplinski†. 2023. Validation of a metabolite-GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases. Frontiers in Plant Science. Volume 14.

 

  1. Karnib, N., Long, B., van Staaden, M., Sprague, J.E., Hall, F.S., Jacobson, D. and Huber, R., 2023. Opiate Sensitivity in Fruit Flies. Medical Research Archives, 11(4).

 

  1. Cashman, M, Melesse Vergara, V., Lane, M., Lagergren, J., Merlet, J., Atkinson, M., Streich, J., Bradburn, C., Plowright, R., Joubert, W., Jacobson D. Longitudinal effects on plant species involved in agriculture and pandemic emergence undergoing changes in abiotic stress. Proceedings of the Platform for Advanced Scientific Computing. 2023. Article No.: 3 Pages 1–10. https://doi.org/10.1145/3592979.3593402

 

  1. Merlet, J., Lagergren, J., Melesse Vergara, V., Cashman, M., Gurley, E., Bradburn, C., Plowright, R., Joubert, W., Jacobson D. Data-driven whole-genome clustering to detect geospatial, temporal, and functional trends in SARS-CoV-2 evolution. Proceedings of the Platform for Advanced Scientific Computing Conference. 2023. Article No.: 26 Pages 1–7

 

  1. Wang, L., Western, D., Timsina, J., Repaci, C., Song, W.M., Norton, J., Kohlfeld, P., Budde, J., Climer, S., Butt, O.H. and Jacobson, D., 2023. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer’s and coronary disease pathways. iScience, 26(4).

 

  1. Ashley-Koch, A.E., Kimbrel, N.A., Qin, X.J., Lindquist, J.H., Garrett, M.E., Dennis, M.F., Hair, L.P., Huffman, J.E., Jacobson, D.A., Madduri, R.K. and Coon, H., 2023. Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program. PLoS genetics, 19(3), p.e1010623.

 

  1. McNaught, K.J., Kuatsjah, E., Zahn, M., Prates, É.T., Shao, H., Bentley, G.J., Pickford, A.R., Gruber, J.N., Hestmark, K.V., Jacobson, D.A. and Poirier, B.C., 2023. Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440. Metabolic Engineering, 76, pp.193-203.

 

  1. Pavicic, M., Mouhu, K., Hautsalo, J., Jacobson, D., Jalli, M. and Himanen, K., Image-based time series analysis to establish differential disease progression for two Fusarium head blight pathogens in oat spikelets with variable resistance. Frontiers in Plant Science, 14, p.796.

 

  1. Kimbrel, N.A., Ashley-Koch, A.E., Qin, X.J., Lindquist, J.H., Garrett, M.E., Dennis, M.F., Hair, L.P., Huffman, J.E., Jacobson, D.A., Madduri, R.K. and Trafton, J.A., 2023. Identification of novel, replicable genetic risk loci for suicidal thoughts and behaviors among US Military Veterans. JAMA psychiatry, 80(2), pp.135-145.

 

  1. Cope, K.R., Prates, E.T., Miller, J.I., Demerdash, O.N., Shah, M., Kainer, D., Cliff, A., Sullivan, K.A., Cashman, M., Lane, M. and Matthiadis, A., Labbé, J., Tschaplinski, T.J., Jacobson, D., Udaya C. Kalluri, U.C. 2023. Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus. Computational and Structural Biotechnology Journal, 21, pp.1122-1139.

 

  1. Lagergren, J., Cashman, M., Melesse Vergara, V., Eller, P., Gazolla, J.G.F.M., Chhetri, H., Streich, J., Climer, S., Thornton, P., Joubert, W. and Jacobson, D., 2022. Climatic clustering and longitudinal analysis with impacts on food, bioenergy, and pandemics. Phytobiomes Journal, (ja).

 

  1. Liu, Y., Yuan, G., Hassan, M.M., Abraham, P.E., Mitchell, J.C., Jacobson, D., Tuskan, G.A., Khakhar, A., Medford, J., Zhao, C. and Liu, C.J., 2022. Biological and Molecular Components for Genetically Engineering Biosensors in Plants. BioDesign Research.

 

  1. Levin, M.G et al. 2023. Genetics of varicose veins reveals polygenic architecture and genetic overlap with arterial and venous disease. Nature Cardiovascular Research, pp.1-14.

 

  1. Kainer, D., Templeton, A.R., Prates, E.T., Jacboson, D., Allan, E.R., Climer, S. and Garvin, M.R., 2023. Structural variants identified using non-Mendelian inheritance patterns advance the mechanistic understanding of autism spectrum disorder. Human Genetics and Genomics Advances, 4(1), p.100150.

 

  1. Špela Tomaž, Marko Petek, Tjaša Lukan, Karmen Pogačar, Katja Stare, Erica Teixeira Prates, Dan Jacobson, Jan Zrimec, Gregor Bajc, Matej Butala, Maruša Pompe-Novak, Quentin Dudley, Nicola Patron, Ajda Taler-Verčič, Aleksandra Usenik, Dušan Turk, Salomé Prat, Anna Coll, and Kristina Gruden. 2022. A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors. Plant Physiology 191, no. 3 (2023): 1934-1952.

 

  1. Tomas Rush, Joanna Tannous, Matthew Lane, Muralikrishnan Gopalakrishnan Meena, Alyssa Carrell, Jacob Golan, Milton Drott, Sylvain Cottaz, Sébastien Fort, Jean-Michel Ané, Nancy Keller, Dale Pelletier, Daniel Jacobson, David Kainer, Paul Abraham, Richard Giannone, and Jesse Labbé. 2022. Lipo-chitooligosaccharides induce specialized fungal metabolite profiles that modulate bacterial growth. Msystems 7, no. 6 (2022): e01052-22. 

 

  1. Hameedi, M.A., T Prates, E., Garvin, M.R., Mathews, I.I., Amos, B.K., Demerdash, O., Bechthold, M., Iyer, M., Rahighi, S., Kneller, D.W. and Kovalevsky, A., … Wakatsuki, S.,* Jacobson, D.*. 2022. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nature Communications. 13, 5285

 

  1. Harfouche, A.L., Nakhle, F., Harfouche, A.H., Sardella, O.G., Dart, E. and Jacobson, D., 2022. A primer on artificial intelligence in plant digital phenomics: embarking on the data to insights journey. Trends in Plant Science.

 

  1. Mehta, K, Cliff, A, Suter, F, Walker, AM, Wolf, M, Jacobson, D, Klasky, S. 2022. Running Ensemble Workflows at Extreme Scale: Lessons Learned and Path Forward. IEEE International Conference on e-Science

 

  1. Abeyratne, C.R., Macaya-Sanz, D., Slavov, G., Gunter, L., Haiby, K., Shuren, R., Chen, J., Jacobson, D., Stanton, B. and DiFazio, S., 2022. High Resolution Analysis of Recombination Rates in Populus trichocarpa. Theoretical and Applied Genetics, 109(3), pp.451-463.

 

  1. Walker, A.M., Cliff, A., Romero, J., Shah, M., Jones, P., Gazolla, J.G.F.M., Jacobson, D. and Kainer, D., 2022. Evaluating the Performance of Random Forest and Iterative Random Forest Based Methods when Applied to Gene Expression Data. Computational and Structural Biotechnology Journal. 20, 3372-3386.

 

  1. Shrestha, V., Chhetri, H.B., Kainer, D., Xu, Y., Hamilton, L., Piasecki, C., Wolfe, B., Wang, X., Saha, M., Jacobson, D. and Millwood, R., The Genetic Architecture of Nitrogen Use Efficiency in Switchgrass (Panicum virgatum L.). Frontiers in Plant Science, p.1216.

 

  1. Yulun Wu, Nicholas Choma, Andrew Chen, Mikaela Cashman, Érica T. Prates, Manesh Shah, Verónica G. Melesse Vergara, Austin Clyde, Thomas S. Brettin, Wibe A. de Jong, Neeraj Kumar, Martha S. Head, Rick L. Stevens, Peter Nugent, Daniel A. Jacobson, James B. Brown, 2022. Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery International Conference on Learning Representations (ICLR)

 

  1. Vasileva, Delyana P., Jared C. Streich, Leah H. Burdick, Dawn M. Klingeman, Hari B. Chhetri, Christa M. Brelsford, J. Christopher Ellis, Dan M. Close, Daniel A. Jacobson*, and Joshua K. Michener*. "Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination." Nucleic Acids Research 50, no. 11 (2022): 6211-6223.

 

  1. Kang I. Ko+, Jean J. Merlet+, Brett P. DerGarabedian, Huang Zhen, Yoko Horiuchi, Eileen Hu, Anh T. Nguyen, Stephen Prouty, Faizan Alawi, Matthew C. Walsh,Yongwon Choi, Sarah E. Millar, Ashley Cliff, Jonathon Romero, Michael R. Garvin, John T. Seykora*, Daniel Jacobson*, Dana T. Graves*. 2022.  NF-kB Perturbation Reveals Unique Immunomodulatory Functions in Prx1+ Fibroblasts that Promote Atopic Dermatitis, Science Translational Medicine. 14, 630, eabj0324, doi:10.1126/scitranslmed.abj0324

 

  1. Kimbrel, N., Ashley-Koch, A., Qin, X., Lindquist, J., Garrett, M., Dennis, M., Hair, L., Huffman, J., Jacobson, D., Madduri, R., Trafton, J., Coon, H., Docherty, A., Kang, J., Mullins, N., Ruderfer, D., Harvey, P., McMahon, B., Oslin, D., Hauser, E., Hauser, M., The DOE-VA Suicide Exemplar Working Group, and Beckham, J. 2021. A Genome-Wide Association Study of Suicide Attempts in the Million Veterans Program Identifies Evidence of Pan-Ancestry and Ancestry-Specific Risk Loci. Molecular Psychiatry, 27(4), pp.2264-2272.

 

  1. Mast, A.E., Wolberg, A.S., Gailani, D., Garvin, M.R., Alvarez, C., Miller, J.I., Jones, P., Aronow, B. and Jacobson, D., 2022. Response to comment on ‘SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung’. Elife, 11, p.e74951.

 

  1. Clerbaux, L.A., Amigó, N., Amorim, M.J., Bal-Price, A., Leite, S.B., Beronius, A., Bezemer, G.F., Bostroem, A.C., Carusi, A., … Jacobson, D., … Coecke, S. Concha, R., … Wittwehr, C. 2022. COVID-19 through adverse outcome pathways: Building networks to better understand the disease–3rd CIAO AOP Design Workshop. ALTEX-Alternatives to animal experimentation, 39(2), pp.322-335.

 

  1. Mullins, N., et al.., 2021. Dissecting the shared genetic architecture of suicide attempt, psychiatric disorders and known risk factors. Biological Psychiatry, 91(3), pp.313-327.

 

  1. Garcia, B.J., Simha, R., Garvin, M., Furches, A., Jones, P., Gazolla, J.G., Hyatt, P.D., Schadt, C.W., Pelletier, D. and Jacobson, D., 2021. A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes. Computational and Structural Biotechnology Journal. 19, pp.5911-5919.

 

  1. Justice, A.C., Gordon, K.S., Romero, J., Edelman, E.J., Garcia, B.J., Jones, P., Khoo, S., Re III, V.L., Rentsch, C.T., Tate, J.P. Tseng, A., Jacobson, D. 2021. Polypharmacy-associated risk of hospitalisation among people ageing with and without HIV: an observational study. The Lancet Healthy Longevity, 2(10), pp.e639-e650.

 

  1. Prates E., Garvin, M.R.,  Jones, P., Miller, J.I.,  Sullivan, K., Cliff, A., Gazolla, J., Shah, M., Walker, A., Lane, M., Rentsch, C., Justice, A., Pavicic, M., Romero, J., Jacobson, D. 2021. Antiviral Strategies Against SARS-CoV-2 - a Systems Biology Approach. Methods in Molecular Biology. SARS-CoV-2 (pp. 317-351)

 

  1. Logan, J., Mehta, K., Cashman, M., Walker, A., Eisenhauer, G., Widener, P., Cliff, A., Jacobson, D.,* Wolf, M.* 2021. Reusability First: Toward FAIR Workflows. Proceedings of IEEE Cluster 2021 Conference.

 

  1. Huber, R. and Jacobson, D.A., 2020. The Phylogenetic Roots of Addiction: Compulsive Drug Seeking, Natural and Drug-Sensitive Reward, and the Acquisition of Learned Habits. Brain, Behavior and Evolution, 95(5), pp.217-221.

 

  1. Stanschewski CS, Rey E, Fiene G, Craine EB, Wellman G, Melino VJ, Patiranage DSR, Johansen K, Schmöckel SM, Bertero D, Oakey H, Colque-Little C, Afzal I, Raubach S, Miller N, Streich J, Amby DB, Emrani N, Warmington M, Mousa MAA, Wu D, Jacobson D, Andreasen C, Jung C, Murphy K, Bazile D, Tester M, on behalf of the Quinoa Phenotyping Consortium. Quinoa Phenotyping Methodologies: An International Consensus. Plants. 2021; 10(9):1759. 

 

  1. Maio, M., Lahn, M., Di Giacomo, A.M., Covre, A., Calabrò, L., Ibrahim, R. Fox, B., et al.2021.  A vision of immuno-oncology: the Siena think tank of the Italian network for tumor biotherapy (NIBIT) foundation. Journal of Experimental & Clinical Cancer Research, 40, Article number: 240.

 

  1. Palmer, R.H.C., Johnson, E.C., Won, H., Polimanti, R., Kapoor, M., Chitre, A., Bogue, M.A., Benca‐Bachman, C.E., Parker, C.C., Ursu, O., Verma, A., Reynolds, T., Ernst, J., Bray, M., Kwon, S.B., Lai, D., Quach, B.C., Gaddis, N.C., Saba, L., Chen, H., Hawrylycz, M., Zhang, S., Zhou, Y., Mahaffey, S., Fischer, C., Sanchez‐Roige, S., Bandrowski, A., Qing, L., Shen, L., Philip, V., Gelernter, J., Bierut, L.J., Hancock, D.B., Edenberg, H.J., Johnson, E.O., Nestler, E.J., Barr, P.B., Prins, P., Smith, D.J., Akbarian, S., Thorgeirsson, T., Walton, D., Baker, E., Jacobson, D., Palmer, A.A., Miles, M., Chesler, E.J., Emerson, J., Agrawal, A., Martone, M. and Williams, R.W. 2021. Integration of Evidence across Human and Model Organism Studies: A Meeting Report. Genes, Brain and Behavior, 20(6), p.e12738. https://doi.org/10.1111/gbb.12738

 

  1. Mast, A.E., Wolberg, A.S., Gailani, D., Garvin, M.R., Alvarez, C., Miller, J.I., Aronow, B. and Jacobson, D., 2021. SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung. Elife, 10, p.e64330.

 

  1. Ramoni, R., Klote, M., Muralidhar, S., Brandt, C., Bernstein, M.A., McMahon, B.H., Jacobson, D.A. and Justice, A.C., 2021. COVID-19 Insights Partnership: Leveraging Big Data from the Department of Veterans Affairs and Supercomputers at the Department of Energy under the Public Health Authority. Journal of the American Medical Informatics Association, 28(7), pp.1578-1581. https://doi.org/10.1093/jamia/ocab062

 

  1. Gerlovin, H., Posner, D., Ho, Y., Rentsch, C., Tate, J., King J., Kurgansky, K., Danciu, I., Costa, L., Linares, F., Goethert, I., Jacobson, D., Freiberg, M., Begoli, E., Muralidhar, S., Ramoni, R., Tourassi, G., Gaziano, M., Justice, A., Gagnon, D., Cho, K. 2021. Pharmacoepidemiology, Machine Learning and COVID-19: An intent-to-treat analysis of hydroxychloroquine, with or without azithromycin, and COVID-19 outcomes amongst hospitalized US Veterans. American Journal of Epidemiology 190, no. 11: 2405-2419.

 

  1. Rentsch, CT, Beckman, JA, Tomlinson, L, Gellad, WF, Alcorn, C, Kidwai-Khan, F, Skanderson, M, Brittain, E, King, JT, Ho, Y, Eden, S, Kundu, S, Lann, MF, Greevy, RA, Ho, PM, Heidenreich, PA, Jacobson, DA, Douglas, IJ, Tate, JP, Evans, SJW, Atkins, D, Justice, AC, Freiberg, MS. Early initiation of prophylactic anticoagulation for prevention of coronavirus disease 2019 mortality in patients admitted to hospital in the United States: cohort study BMJ 2021; 372 :n311

 

  1. Wada, A., Prates, É.T., Hirano, R., Werner, A.Z., Kamimura, N., Jacobson, D.A., Beckham, G.T. and Masai, E., 2021. Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics. Metabolic Engineering, 64 (2021): 167-179.

 

  1. Pavicic, M., Overmyer, K., Jones, P., Jacobson, D. and Himanen, K., 2021. Image-Based Methods to Score Fungal Pathogen Symptom Progression and Severity in Excised Arabidopsis Leaves. Plants, 10(1), p.158.

 

  1. Inkster, B. et al, 2020. Early warning signs of a mental health tsunami: A coordinated response to gather initial data insights from multiple digital services providers. Frontiers in Digital Health, 2, p.64.

 

  1. Garvin, M.R., Prates, E.T., Pavicic, M., Jones, P., Amos, B.K., Geiger, A., Shah, M.B., Streich, J., Gazolla, J.G.F.M., Kainer, D. Cliff, A., Romero, J., Keith, N., Brown, J., Jacobson, D. 2020. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biology, 21(1), pp.1-26.

 

  1. Hofmeister, B.T., Denkena, J., Colomé-Tatché, M., Shahryary, Y., Hazarika, R., Grimwood, J., Mamidi, S., Jenkins, J., Grabowski, P.P., Sreedasyam, A. and Shu, S., Barry, K., Lail, K., Adam, C., Lipzen, A., Sorek, R., Kudrna, D., Talag, J., Wing, R., Hall, D., Jacobson, D., Tuskan, G., Schmutz, J., Johannes, F., Schmitz, R. 2020. A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biology, 21(1), pp.1-27.

 

  1. Kelley, B.R., Ellis, J.C., Large, A., Schneider, L.G., Jacobson, D. and Johnson, J.G., 2020. Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee. Frontiers in Microbiology, 11.

 

  1. Baer, A.G., Bourdon, A.K., Price, J.M., Campagna, S.R., Jacobson, D.A., Baghdoyan, H.A. and Lydic, R., 2020. Isoflurane anesthesia disrupts the cortical metabolome. Journal of Neurophysiology, 124(6), pp.2012-2021.

 

  1. Divgi, C., Carrasquillo, J.A., Meredith, R., Seo, Y., Frey, E.C., Bolch, W.E., Zimmerman, B.E., Akabani, G., Jacobson, D.A., Brown, B. and Davern, S.M., 2020. Overcoming Barriers to Radiopharmaceutical Therapy: An Overview from the NRG-NCI Working Group on Dosimetry of Radiopharmaceutical Therapy (RPT). International Journal of Radiation Oncology, Biology, Physics.

 

  1. Garvin, M.R., Alvarez, C., Miller, J.I., Prates, E.T., Walker, A.M., Amos, B.K., Mast, A.E., Justice, A., Aronow, B. and Jacobson, D., 2020. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. Elife, 9, p.e59177.

 

  1. Zhang, X., Baer, A.G., Price, J.M., Jones, P.C., Garcia, B.J., Romero, J., Cliff, A.M., Mi, W., Brown, J.B., Jacobson, D.A., Lydic, R., Baghdoyan, H. A. 2020. Neurotransmitter networks in mouse prefrontal cortex are reconfigured by isoflurane anesthesia. Journal of neurophysiology, 123(6), pp.2285-2296.

 

  1. Chhetri, H.B., Furches, A., Macaya-Sanz, D., Walker, A.R., Kainer, D., Jones, P., Harman-Ware, A.E., Tschaplinski, T.J., Jacobson, D., Tuskan, G.A. and DiFazio, S.P., 2020. Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa. Frontiers in plant science, 11, p.1391.

 

  1. King Jr, J.T., Yoon, J.S., Rentsch, C.T., Tate, J.P., Park, L.S., Kidwai-Khan, F., Skanderson, M., Hauser, R.G., Jacobson, D.A., Erdos, J.  Cho, K., 2020. Development and validation of a 30-day mortality index based on pre-existing medical administrative data from 13,323 COVID-19 patients: The Veterans Health Administration COVID-19 (VACO) Index. PloS One, 15(11), p.e0241825.

 

  1. Prates, E.T., Garvin, M.R., Pavicic, M., Jones, P., Shah, M., Demerdash, O., Amos, B.K., Geiger, A. and Jacobson, D., 2021. Potential pathogenicity determinants identified from structural proteomics of SARS-CoV and SARS-CoV-2. Molecular Biology and Evolution, 38(2), pp.702-715.

 

  1. Streich, J., Romero, J., Gazolla, J.G.F.M., Kainer, D., Cliff, A., Prates, E.T., Brown, J.B., Khoury, S., Tuskan, G.A., Garvin, M. and Jacobson, D.*, Harfouche A*., 2020. Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals? Current Opinion in Biotechnology, 61, pp.217-225.

 

  1. Kankanala, P., Jones, P., Nandety, R.S., Jacobson, D.A. and Mysore, K.S., 2020. Plasticity of Phymatotrichopsis omnivora infection strategies is dependent on host and nonhost plant responses. Plant, Cell & Environment. 1– 18.

 

  1. Alexandersson, E., Kushwaha, S., Weighill, D., Climer, S., Jacobson, D., and Andreasson, E. (2020). Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. BMC Plant Biology 20: 120; doi: 10.21203/rs.2.15738/v3

 

  1. Cliff, A., Romero, J., Kainer, D., Walker, A., Furches, A. and Jacobson, D., 2019. A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks. Genes, 10(12), p.996.

 

  1. Furches, A., Kainer, D., Weighill, D., Large, A., Jones, P., Walker, A.M., Romero, J., Gazolla, F.M., Gabriel, J., Joubert, W. Shah, M., Streich, J., Ranjan, P., Schmutz, J., Sreedasyam, A., Macaya-Sanz, D, Zhao, N., Martin, MZ., Rao, X., Dixon, RA., DiFazio, S., Tschaplinski, TJ., Chen, J., Tuskan, GA., Jacobson D. 2019. Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. Frontiers in plant science, 10, p.1249.

 

  1. Weighill, D., Tschaplinski, T., Tuskan, G. and Jacobson, D., 2019. Data Integration in Poplar:‘Omics Layers and Integration Strategies. Frontiers in Genetics, 10, p.874.

 

  1. Harfouche A, Jacobson D, Kainer D, Romero J, Harfouche AH, Scarascia Mugnozza G, Moshelion M, Tuskan G, Keurentjes J, Altman A. 2019. Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence. Trends in Biotechnology.  Selected for cover.

 

  1. Jones, P., Garcia, B.J., Furches, A., Tuskan, G.A. and Jacobson, D., 2019. Plant host-associated mechanisms for microbial selection. Frontiers in Plant Science, 10.

 

  1. Labbé J, Muchero W, Czarnecki O, Wang J, Wang X, Bryan A, Zheng K, Yang Y, Xie M, Zhang J, Wang D, Meidl P, Wang H, Morrell-Falvey J, Cope K, Maia L, Ané J-M, Mewalal R, Jawdy S, Gunter L, Schackwitz W, Martin J, Le Tacon F, Li T, Zhang Z, Ranjan P, Lindquist E, Yang X, Jacobson D, Tschaplinski T, Barry K, Schmutz J, Chen J-G, Tuskan G. 2019. Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase. Nature Plants.  5(7), pp.676-680.

 

  1. Weighill D, Jones P, Bleker C, Ranjan P, Shah M, Zhao N, Martin M, DiFazio S, Macaya-Sanz D, Schmutz J, Sreedasyam A, Tschaplinski T, Tuskan G, Jacobson D. Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships. Front Genet. 2019 May 10;10:417.

 

  1. Weighill, D., Macaya-Sanz, D., DiFazio, S. P., Joubert, W., Shah, M., Schmutz, J., ... & Jacobson, D. (2019). Wavelet-based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. Frontiers in Genetics, 10, 487.

 

  1. Yaw, A.M., Prosser, R.A., Jones, P.C., Garcia, B.J., Jacobson, D.A. and Glass, J.D., 2019. Epigenetic Effects of Paternal Cocaine on Reward Stimulus Behavior and Accumbens Gene Expression in Mice. Behavioural Brain Research. doi.org/10.1016/j.bbr.2019.02.043.

 

  1. Chhetri, H., Macaya-Sanz, D., Kainer, D., Biswal, A., Chen, J., Collins, C., Evans, L., Hunt, K., Mohnaty, S., Rosenstiel, T., Ryno, D., Winkeler, K., Yang, X., Jacobson, D., Mohnen, D., Muchero, W., Strauss, S., Tschaplinski, T., Tuskan, G., DiFazio, S. 2019. Multi-trait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytologist.  doi:10.1111/nph.15777

 

  1. Bonito, G.M., Benucci, G.M.N., Hameed, K., Weighill, D., Jones, P., Chen, K.H., Jacobson, D., Schadt, C.W. and Vilgalys, R., 2019. Fungal-bacterial networks in the Populus rhizobiome are impacted by soil properties and host genotype. Frontiers in Microbiology, 10, p.481.

 

  1. Garcia, B.J., Labbe, J., Jones, P., Abraham, P., Hodge, I., Climer, S., Jawdy, S., Gunter, L., Tuskan, G., Yang, X. Tschaplinski, T., Jacobson, D., 2018. Phytobiome and transcriptional adaptation of Populus deltoides to acute progressive drought and cyclic drought. Phytobiomes Journal 2018 2:4, 249-260

 

  1. Tuskan GA, Groover AT, Schmutz J, DiFazio SP, Myburg A, Grattapaglia D, Smart LB, Yin T, Aury JM, Kremer A, Leroy T, Le Provost G, Plomion C, Carlson JE, Randall J, Westbrook J, Grimwood J, Muchero W, Jacobson D, Michener JK. Hardwood Tree Genomics: Unlocking Woody Plant Biology. Front Plant Sci. 2018 Dec 17;9:1799.

 

  1. Decker, S.R., Harman-Ware, A.E., Happs, R.M., Wolfrum, E.J., Tuskan, G.A., Kainer, D., Oguntimein, G., Rodriguez, M., Weighill, D., Jones, P.C. and Jacobson, D., 2018. High Throughput Screening Technologies in Biomass Characterization. Frontiers in Energy Research, 6, p.120.

 

  1. van Wyk, F., Khojandi, A., Williams, B., MacMillan, D., Davis, R.L., Jacobson, D.A. and Kamaleswaran, R., 2018. A Cost-Benefit Analysis of Automated Physiological Data Acquisition Systems Using Data-Driven Modeling. Journal of Healthcare Informatics Research, pp.1-19.

 

  1. Joubert, W., Weighill, D., Kainer, D.,  Climer, S., Justice A, Fagnan K., and Jacobson, D., 2018.  Gordon Bell Prize Winner: Attacking the Opioid Epidemic: Determining the Epistatic and Pleiotropic Genetic Architectures for Chronic Pain and Opioid Addiction. SC '18 Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis Article No. 57

 

  1. Joubert, W., Nance, J., Climer, S., Weighill, D., & Jacobson, D. (2019). Parallel Accelerated Custom Correlation Coefficient Calculations for Genomics Applications. Parallel Computing, 84, 15-23

 

  1. Joubert, W., Nance, J., Weighill, D. and Jacobson, D., “Parallel Accelerated Vector Similarity Calculations for Genomics Applications. Parallel Computing, Parallel Computing, 75, 130-145. doi.org/10.1016/j.parco.2018.03.009. (2018).

 

  1. Weighill, D, Jones, P, Shah, M, Ranjan, P, Muchero, W, Schmutz, J, Sreedasyam, A, Macaya-Sanz, D, Sykes, R, Zhao, N, Martin, M, DiFazio, S, Tschaplinski, T, Tuskan, G, Jacobson, D. “Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery.” Frontiers in Energy Research 6 (2018): 30

 

  1. Torres-Cortes, G., Garcia, B.J., Compant, S., Rezki, S., Jones, P., Preveaux, A., Briand, M., Roulet, A., Bouchez, O., Jacobson, D. and Barret, M., 2019. Differences in resource use lead to coexistence of seed-transmitted microbial populations. Scientific reports, 9(1), p.6648.

 

  1. Kelley, B.R., Ellis, J.C., Hyatt, D., Jacobson, D. and Johnson, J., 2018. Isolation and Whole‐Genome Sequencing of Environmental Campylobacter. Current protocols in microbiology, 51(1), p.e64.

 

  1. Tuskan, G.A., Mewalal, R., Gunter, L.E., Palla, K.J., Carter, K., Jacobson, D.A., Jones, P.C., Garcia, B.J., Weighill, D.A., Hyatt, P.D. and Yang, Y., 2018. Defining the genetic components of callus formation: A GWAS approach. PloS one, 13(8), p.e0202519.

 

  1. Bryan, A.C., Zhang, J., Guo, J., Ranjan, P., Singan, V., Barry, K., Schmutz, J., Weighill, D., Jacobson, D., Jawdy, S. and Tuskan, G.A., 2018. A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. G3: Genes, Genomes, Genetics, pp.g3-200188.

 

  1. Laura L Lee, Sara E Blumer-Schuette, Javier A Izquierdo, Jeffrey V Zurawski, Andrew J Loder, Jonathan M Conway, James G Elkins, Mircea Podar, Alicia Clum, Piet C Jones, Marek J Piatek, Deborah A Weighill, Daniel A Jacobson, Michael WW Adams, Robert M Kelly. 2018. Genus-wide assessment of lignocellulose utilization in the extremely thermophilic Caldicellulosiruptor by genomic, pan-genomic and metagenomic analysis. Applied and environmental microbiology, pp.AEM-02694.

 

  1. Abraham, P.E., Garcia, B.J., Gunter, L.E., Jawdy, S.S., Engle, N., Yang, X., Jacobson, D.A., Hettich, R.L., Tuskan, G.A. and Tschaplinski, T.J., Jacobson, D. 2018. Quantitative proteome profile of water deficit stress responses in eastern cottonwood (Populus deltoides) leaves. PloS one, 13(2), p.e0190019.

 

  1. Kathryn Petersen Mace, Daniel Jacobson, Brooklin Gore, Lauren Rotman, Jennifer Schopf, Mary Hester, Predrag Radulovic, William Barnett. 2017. Report from the 2016 CrossConnects workshop: improving data mobility & management for bioinformatics. Standards in Genomic Sciences, 12, 83.

 

  1. Xiaohan Yang,, Rongbin Hu, Hengfu Yin, Jerry Jenkins, Shengqiang Shu, Haibao Tang, Degao Liu, Deborah A. Weighill, Won Cheol Yim, Jungmin Ha, Karolina Heyduk, David M. Goodstein, Hao-Bo Guo, Robert C. Moseley, Elisabeth Fitzek, Sara Jawdy, Zhihao Zhang, Meng Xie, James Hartwell, Jane Grimwood, Paul E. Abraham, Ritesh Mewalal, Juan D. Beltr_an, Susanna F. Boxall, Louisa V. Dever, Kaitlin J. Palla, Rebecca Albion, Travis Garcia, Jesse Mayer, Sung Don Lim, Ching Man Wai, Paul Peluso, Robert Van Buren, Henrique Cestari De Paoli, Anne M. Borland, Hong Guo, Jin-Gui Chen, Wellington Muchero, Yanbin Yin, Daniel A. Jacobson, Timothy J. Tschaplinski, Robert L. Hettich, Ray Ming, Klaus Winter, James H. Leebens-Mack, J. Andrew C. Smith, John Cushman, Jeremy Schmutz, Gerald A. Tuskan. 2017. The Kalanchoe genome provides insights into the evolution of crassulacean acid metabolism. Nature communications, 8(1), pp.1-15.

 

  1. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project.  Weston, David; Turetsky, Merritt; Johnson, Matthew; Granath, Gustaf; Lindo, Zoe; Belyea, Lisa; Rice, Steven; Hanson, David; Engelhardt, Katharina; Schmutz, Jeremy; Dorrepaal, Ellen; Euskirchen, Eugenie; Stenøien, Hans; Szövényi, Péter ; Jackson, Michelle; Piatkowski, Bryan; Muchero, Wellington; Norby, Richard; Kostka, Joel; Glass, Jennifer; Rydin, H; Limpens, Juul; Tuittila, Eeva Stiina; Ullrich, Kristian; Carrell, Alyssa; Benscoter, Brian; Chen, Jin-Gui; Oke, Tobi; Nilsson, Mats; Ranjan, Priya; Jacobson, Daniel; Lilleskov, Erik; Clymo, RS; Shaw, A. Jonathan. New Phytologist , 217(1), pp.16-25.

 

  1. Weighill DA, Jacobson DA. (2016)  Network Metamodeling: The Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology.   Book Chapter, Adv Biochem Eng Biotechnol. DOI: 10.1007/10_2016_46

 

  1. Paul E. Abraham, Hengfu Yin, Anne M. Borland, Deborah Weighill, Sung Don Lim, Henrique Cestari De Paoli, Nancy Engle, Piet C. Jones, Ryan Agh, David J. Weston, Stan D. Wullschleger, Timothy Tschaplinski, Daniel Jacobson, John C. Cushman, Robert L. Hettich, Gerald A. Tuskan, Xiaohan Yang. (2016) Temporal dynamics of transcripts, proteins, and metabolites that define crassulacean acid metabolism in Agave. Nature Plants 2, Article number: 16178 (2016) doi:10.1038/nplants.2016.178. Selected for cover.

 

  1. Kaijie Zheng, Xiaoping Wang, Deborah Weighill, Hao-Bo Guo, Meng Xie, Yongil Yang, Jun Yang, Shucai Wang, Daniel Jacobson, Hong Guo, Wellington Muchero, Gerald Tuskan, and Jin-Gui Chen. (2016) Characterization of DWARF14 Genes in Populus. Scientific Reports 6:21593 | doi: 10.1038/srep21593

 

  1. Coetzee, C., Brand, J., Jacobson, D., & Du Toit, W. J. (2016). Sensory effect of acetaldehyde on the perception of 3‐mercaptohexan‐1‐ol and 3‐isobutyl‐2 methoxypyrazine. Australian Journal of Grape and Wine Research. | doi: 10.1111/ajgw.12206

 

  1. Young, P., Eyeghe-Bickong, H. A., du Plessis, K., Alexandersson, E., Jacobson, D. A., Coetzee, Z. A., Deloire, A., Vivier, M. A. (2015). Grapevine plasticity in response to an altered microclimate: Sauvignon Blanc modulates specific metabolites in response to increased berry exposure. Plant Physiology . doi:10.1104/pp.15.01775

 

  1. Setati ME, Jacobson D and Bauer FF (2015). Sequence-based analysis of the Vitis vinifera L. cv Cabernet Sauvignon grape must mycobiome in three South African vineyards employing distinct agronomic systems. Front. Microbiol. 6:1358. doi: 10.3389/fmicb.2015.01358

 

  1. Weighill DA, Jacobson DA. (2015) 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. PLoS Comput Biol 11(3): e1004079. doi: 10.1371/journal.pcbi.1004079.

 

  1. Monforte, A. R., Jacobson, D., & Silva Ferreira, A. C. (2015). Chemiomics: Network Reconstruction and Kinetics of Port Wine Aging. Journal of agricultural and food chemistry, 63(9), 2576-2581.

 

  1. Whitener, M. E. B., Carlin, S., Jacobson, D., Weighill, D., Divol, B., Conterno, L., ... & Vrhovsek, U. (2015). Early fermentation volatile metabolite profile of non-Saccharomyces yeasts in red and white grape must: a targeted approach. LWT-Food Science and Technology.

 

  1. Coetzee, C., Brand, J., Emerton, G., Jacobson, D., Silva Ferreira, A.C. and du Toit, W.J. (2015), Sensory interaction between 3-mercaptohexan-1-ol, 3-isobutyl-2-methoxypyrazine and oxidation-related compounds. Australian Journal of Grape and Wine Research. doi: 10.1111/ajgw.12133

 

  1. Alexandersson E, Jacobson D, Vivier M, Weckwerth W and Andreasson E. "Field-omics" – understanding large-scale molecular data from field crops. Front. Plant Sci. 5:286, 2014

 

  1. Fairbairn S, Smit A, Jacobson D, Prior B, Bauer F. Environmental Stress and Aroma Production During Wine Fermentation.  S. Afr. J. Enol. Vitic., 35:168-177, 2014

 

  1. Bengtsson T, Weighill D, Proux-Wéra E, Levander F, Resjö S, Burra DD, Moushib LI,  Hedley PE, Liljeroth E, Jacobson D, Alexandersson E and E Andreasson. Proteomics and Transcriptomics of the BABA-Induced Resistance Response in Potato Using a Novel Functional Annotation Approach. BMC Genomics. 15:315, 2014

 

  1. van Wyngaard, E., Brand, J., Jacobson, D. & du Toit, W. Sensory interaction between 3-mercaptohexan-1-ol and 2-isobutyl-3-methoxypyrazine in dearomatised Sauvignon Blanc wine. Aust. J. Grape Wine Res. 20, 178–185, 2014

 

  1. Marx IJ, van Wyk N, Smit S, Jacobson D, Viljoen-Bloom M, Volschenk H. Comparative secretome analysis of Trichoderma asperellum S4F8 and Trichoderma reesei Rut C30 during solid-state fermentation on sugarcane bagasse. Biotechnology for Biofuels.  6, pp 172, 2013

 

  1. Jacobson D., Monforte, A.R., Silva Ferreira A.C., Untangling the chemistry of Port wine aging with the use of GC-FID, multivariate statistics and network reconstruction, Journal of Agricultural and Food Chemistry, 61 (10), pp 2513–2521, 2013

 

  1. Setati ME, Jacobson D, Andong UC, Bauer F, The vineyard yeast microbiome, a mixed model microbial map., PloS One, 7,  e52609, 2012

 

  1. Young P, Lashbrooke J, Alexandersson E, Jacobson D, Moser C, Velasco R, Vivier M, The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera, BMC Genomics, 13,  243, 2012

 

  1. Jacobson D, Emerton G, GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network, BMC Bioinformatics, 13,  197, 2012

 

  1. Styger G, Jacobson D. Prior B. Bauer F, Genetic analysis of the metabolic pathways responsible for aroma metabolite production by Saccharomyces cerevisiae., Applied microbiology and biotechnology,  1-14, 2012

 

  1. Rossouw D, Jolly N, Jacobson D, Bauer F, The effect of scale on gene expression: commercial versus laboratory wine fermentations, Applied microbiology and biotechnology, 93,  1207-1219, 2012

 

  1. Rossouw D, Jacobson D, Bauer F, Transcriptional regulation and the diversification of metabolism in wine yeast strains, Genetics, 190,  251-261, 2012

 

  1. Young, P., E. Alexandersson, D. Jacobson, J. Lashbrooke, Z. Coetzee, A. Deloire, and M. Vivier. The molecular and metabolite profiling of grapevine berries in a model vineyard where the microclimate of the developing bunches has been altered.  South African Journal of Botany, vol. 79, pp. 223-223, 2012.

 

  1. Bester M, Jacobson D, Bauer F, Many Saccharomyces cerevisiae Cell Wall Protein Encoding Genes Are Coregulated by Mss11, but Cellular Adhesion Phenotypes Appear Only Flo Protein Dependent., G3, 2,  131-141, 2012

 

  1. Sharathchandra R, Stander C, Jacobson D, Ndimba B, Vivier M, Proteomic analysis of grape berry cell cultures reveals that developmentally regulated ripening related processes can be studied using cultured cells., PloS One, 6,  e14708, 2011

 

  1. Alexandersson E, Becker J, Jacobson D, Nguema-Ona E, Steyn C, Denby K, Vivier M, Constitutive expression of a grapevine polygalacturonase-inhibiting protein affects gene expression and cell wall properties in uninfected tobacco., BMC Research notes, 4,  493, 2011

 

  1. Styger G, Jacobson D, Bauer F, Identifying genes that impact on aroma profiles produced by Saccharomyces cerevisiae and the production of higher alcohols., Applied microbiology and biotechnology, 91,  713-730, 2011

 

  1. Rossouw D, van den Dool A, Jacobson D, Bauer F, Comparative transcriptomic and proteomic profiling of industrial wine yeast strains. Applied and environmental microbiology, 76,  3911-3912, 2010

 

  1. Opara UL, Jacobson D, Al-Saady NA, Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses., Journal of Zhejiang University. Science. B, 11,  332-341, 2010

 

  1. O'Neill K, Garcia A, Schwegmann A, Jimenez R, Jacobson D, Hermjakob H, OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. BMC Bioinformatics, 9,  437, 2008

 

  1. O’Neill, K., Schwegmann, A., Jimenez, R., Jacobson, D. and Garcia, A., 2007. OntoDas-integrating DAS with ontology-based queries. Ontology Design Patterns for Bio-Ontologies – Proceedings from The 10th Annual Bio-Ontologies Meeting.

 

  1. O’Neill, K., Garcia-Castro, A., and Jacobson, D., 2007. Knowledge Driven User Interfaces for Complex Biological Queries. Proceedings of SABioinf, pp.111-115.

 

  1. Anagnostopoulos, A.V, and D. Jacobson. It's a knockout! 1996. Trends in Genetics 12: 236. https://doi.org/10.1016/0168-9525(96)30054-1

 

  1. Jacobson, D. and A. Anagnostopoulos. 1996. Internet resources for transgenic or targeted mutation research. Trends in Genetics 12: 117-118. https://doi.org/10.1016/0168-9525(96)81425-9

 

  1. D. Jacobson 1994.  The World Wide Web for biologists, Protein Science 3: 2159-2161.

 

  1. Woychik, R.P., Wassom, J.S., Kingsbury, D. and D.A. Jacobson. TBASE: a computerized database for transgenic animals and targeted mutations, 1993.  Nature 636: 375-376.

 

  1. Jacobson, K.B., Arlinghaus, H.F., Schmitt, H., Sachleben, R.A., Brown, G.M., Thonnard, N., Sloop, F.V., Foote, R.S., Larimer, F.W., Woychik, R.P., England, M.W., Burchett, K.L. and D.A. Jacobson. 1991.  An approach to the use of stable isotopes for DNA sequencing, Genomics 9: 51-59.

 

  1. McCarthy, J. F., Jacobson, D. A., Shugart, L. R. & Jimenez, B. D. Pre-exposure to 3-methylcholanthrene increases benzo[a]pyrene adducts on DNA of bluegill sunfish. Marine Environmental Research 28, 323–328 (1989).

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